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Allostery in Its Many Disguises: From Theory to Applications
Related publications (33)
Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance
Sebastian Maerkl, Shiyu Cheng, Ivan Istomin, Maria Lopez Malo, Amir Shahein, Evan James Olson
Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription fac ...
NATURE PORTFOLIO2022Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2021Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters
Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...
EPFL2020Mechanistic insights into AMP-activated protein kinase-dependent gene expression
AMP-activated protein kinase (AMPK) is a fundamental enzyme that controls energy homeostasis, through orchestrating the cellular response to a reduction in energy availability. Under conditions of cellular energy stress AMPK senses the decrease in ATP leve ...
EPFL2019Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells
Felix Naef, David Michael Suter, Torgil Elias Friman, Onur Tidin
The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcript ...
2019A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family
Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot
TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcript ...
2019ORGANOHALIDE RESPIRATION: STUDY OF THE MEMBRANE PROTEIN COMPLEX RESPONSIBLE FOR THE REDUCTION OF HALOGENATED COMPOUNDS
Christof Holliger, Julien Maillard, Adrian Schmid, Lorenzo Cimmino
Organohalide respiration (OHR) is a bacterial anaerobic respiratory process in which halogenated compounds are used as terminal electron acceptors. Desulfitobacterium and Dehalobacter, paradigmatic organohalide-respiring bacteria (OHRB), harbour the pceABC ...
2019Mitocellular communication: Shaping health and disease
Johan Auwerx, Sébastien Robert Victor Herzig, Adrienne Joëlle Laurence Mottis
Throughout the animal kingdom, mitochondria are the only organelles that retain their own genome and the transcription and translation machineries that are all essential for energy harvesting. Mitochondria have developed a complex communication network, al ...
AMER ASSOC ADVANCEMENT SCIENCE2019Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells
Cells live in ever-changing environments, thereby facing a variety of dynamic environmental signals. Environmental stimuli elicit intracellular responses through signaling pathways, which converge on transcriptional activation or repression of target genes ...
EPFL2018Modeling and analysis of parts and devices of genetic regulation
DNA encrypts the composition of the cellular material that is synthesized through transcription and translation. Never-theless, gene regulation mechanisms determine the final amount of transcribed and translated material. Transcription factors (TF) are a c ...
EPFL2018